Hi Jim, MiBIG is a useful database of natural product gene clusters and structures, which you can download in JSON format here, and use pretty easily from within Python: https://mibig.secondarymetabolites.org/repository.html This also includes pathway and organism information.
Secondly, our ClusterCAD database is built with RDKit and Django, but only includes Type I modular PKSs imported from MiBIG. You can use it online at clustercad.jbei.org, or view the code and launch a docker install locally from https://github.com/JBEI/clusterCAD. Internally, it has a RDKit postgresql database, and includes predicted chemical intermediates at each step of biosynthesis in addition to final products. It is hand curated, to improve on the automatic AntiSMASH annotations in MiBIG. I will gradually expand this to support a greater diversity of natural products. I could send you an example Jupyter notebook for using it programatically. Sincerely, Tyler On Mon, Nov 27, 2017 at 1:30 PM, James T. Metz via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net> wrote: > RDkit Discussion Group, > > My apologies in advance if my request is not appropriate for this > discussion group. > > Given a small molecule that might have some resemblance to natural > products, > can someone suggest a free, comprehensive, PYTHON/RDkit searchable database > of natural products that might be suitable for similarity and substructure > searching. > > I am aware of a few websites that permit searching on the website. If > possible, > I would like to programmatically search by running a PYTHON/RDkit script on > my > local machine and then return the structures of related molecules to my > local script. > > I would prefer not having to download and store a huge database. > > Also, if possible, it would be important to return the organism(s) that > creates > the natural product. Pathway information would be also very, very helpful. > > I greatly welcome comments and suggestions. > > Thank you. > > Regards, > Jim Metz > Northwestern University > > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Tyler W. H. Backman Postdoctoral Fellow Lawrence Berkeley National Laboratory Joint BioEnergy Institute ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
